We present a molecular phylogeny of Rhinatrematidae on the basis of three mitochondrial and four nuclear genes and describe two new species of Rhinatrema from the Guianan region of Brazil, both of which were previously conflated with R. ron. Our phylogenetic results show that at least one species of Epicrionops is nested within the Rhinatrema clade. Although our taxon sampling is limited, we reallocated E. niger in the genus Rhinatrema in order to avoid paraphyly. The phylogeny supports our new species described here. One of the new species is closely related to R. bivittatum in a clade that also includes R. shiv. The other new species is sister to all other sampled Rhinatrema and is morphologically similar to R. ron but differs in number of annuli and in the condition of the oral mucosa. The known distribution of R. ron is now restricted to the type locality.